get_rarecurve: obtain the result of rare curve

In MicrobiotaProcess: an R package for analysis, visualization and biomarker discovery of microbiome

Description

generate the result of rare curve.

Usage

get_rarecurve(obj, ...)

## S4 method for signature 'data.frame'
get_rarecurve(obj, sampleda, factorLevels = NULL, chunks = 400)

## S4 method for signature 'phyloseq'
get_rarecurve(obj, ...)

Arguments

obj	phyloseq class or data.frame shape of data.frame (nrow sample * ncol feature)
...,	additional parameters.
sampleda	data.frame, (nrow sample * ncol factor)
factorLevels	list, the levels of the factors, default is NULL, if you want to order the levels of factor, you can set this.
chunks	integer, the number of subsample in a sample, default is 400.

Details

This function is designed to calculate the rare curve result of otu table the result can be visualized by 'ggrarecurve'.

Value

rarecurve class, which can be visualized by ggrarecurve

Author(s)

Shuangbin Xu

Examples

data(test_otu_data)
set.seed(1024)
res <- get_rarecurve(test_otu_data, chunks=200)
p <- ggrarecurve(obj=res, 
                 indexNames=c("Observe","Chao1","ACE"),
                 shadow=FALSE,
                 factorNames="Group")

MicrobiotaProcess documentation built on April 18, 2021, 6 p.m.